docs: def _hmm_command(self, input_pipe, pairs_to_run):
          r"""INTERNAL method for getting cmdline for running a batch of HMMs.
  
          Parameters
          ----------
          input_pipe: as hmmsearch
          pairs_to_run: list
              list with 2 members: (1) list of hmm and output file, (2) number of
              CPUs to use when searching
  
          Returns
          -------
          A string command to be run with bash
          """
          element = pairs_to_run.pop()
          hmmsearch_cmd = self._individual_hmm_command(element[0][0],
                                                        element[0][1],
                                                        element[1])
          while len(pairs_to_run) > 0:
              element = pairs_to_run.pop()
              hmmsearch_cmd = "tee >(%s) | %s" % (self._individual_hmm_command(element[0][0],
                                                                                element[0][1],
                                                                                element[1]),
                                                  hmmsearch_cmd)
  
          # Run the actual command
          hmmsearch_cmd = "%s | %s" % (input_pipe, hmmsearch_cmd)
          return hmmsearch_cmd